Figure 3

Standards for MspI digestion and progressive PCR. A) MspI digestion of human genomic DNA isolated from human post-mortem brain tissues. DNA (200 ng) was digested by MspI and run on a 4–20% precast polyacrylamide gel and stained with EtBr. Arrows show three satellite DNA bands characteristic of this enzymatic digestion. B) Agilent 2100 Bioanalyzer chromatogram of MspI digested genomic DNA. C) Bioanalyzer 2100 image of a single library from an MspI digested DNA sample. Notice that the satellite bands (indicated by arrows) are still visible on the Bioanalyzer image. D) Progressive PCR amplification combined with limited PCR extension time allows for size selection and amplification of six bisulfite converted libraries (Lanes 1–5 are distinct RRBS libraries; lane 6 (‘C’) is a negative control). After different progressive PCR cycles (18X, 22X, 24X, or 26X – the same libraries are shown for each cycle number) band intensity increases as cycle number increases. Arrows indicate the three satellite DNA bands that are still visible in these libraries.